Uncovering the Rules of DNA’s Hidden Language

By Keith Gillogly

What determines a cell’s identity isn’t the genes within but how they’re used. To read and interpret this genetic material, cells rely on transcription factors. These proteins bind to specific regions of DNA known as regulatory sequences, telling genes when to activate or stay silent. This process informs everything from normal cell differentiation to cancer onset to neurodegeneration.

Michael Buck, PhD, professor of biochemistry in the Jacobs School of Medicine and Biomedical Sciences, has long sought to understand these regulatory signals and how this information flows from the DNA. To continue this research, Buck was recently awarded a five-year, $2.2 million grant from the National Institute of General Medical Sciences, part of the National Institutes of Health.

The grant is a Maximizing Investigators’ Research Award (MIRA), which provides flexible support for promising investigators’ deeper exploration. 

Buck’s research project, titled “Defining the Rules for Pioneer Factor Nucleosome Engagement,” focuses on pioneer factors, a type of transcription factor that can bind to DNA even when it’s tightly wrapped around spools of protein called nucleosomes.

Transcription factors readily bind to more accessible and exposed stretches of DNA to activate genes. But since pioneer factors penetrate the coils of hidden genetic material, they can activate otherwise silent genes.

Now, Buck and his colleagues are working to uncover the molecular rules enabling pioneer factors to recognize, bind to, and activate these hidden regulatory sequences.

Yet, transcription factors are but one mechanism affecting gene activation. Buck and his team want to also understand how pioneering transcription factors interact with the epigenetic code.

Cells must respond to environmental stresses from behaviors and the environment, like exposure to pollutants or changing diet. The resulting chemical changes influence gene activity, even without altering the DNA sequence. 

Known as epigenetic changes, these chemical tags can make genes more or less accessible for transcription, augmenting or limiting gene activity. Disease onset, infection, and many other conditions can all influence gene activity.

“If you have a certain disease or a viral infection, all of those things are going to leave an epigenetic mark,” Buck says. “And the consequences of those marks are going to affect the downstream activation of certain genes.”

To investigate these mechanisms, Buck’s team has developed a high-throughput experimental platform called Pioneer-seq, which enables simultaneously examining thousands of DNA–nucleosome interactions and how they’re bound by transcription factors.

By mixing purified DNA and proteins in precise laboratory conditions, the system models what happens inside the nucleus and measures how well different transcription factors bind to their targets.

From there, the researchers can model nucleosomes containing various epigenetic changes. “Understanding these epigenetic modifications is really important,” Buck says. “So, we can add those epigenetic modifications and ask, how do they directly affect binding?”

Using Pioneer-seq, the research team can pinpoint conditions such as DNA sequence, position within the nucleosome, and chemical modifications that govern the effectiveness of transcription factor binding.

Many diseases, like cancer, set in when transcription factors improperly regulate genes. Therefore, more advanced knowledge of transcription factor binding is essential to restoring proper gene regulation.

Buck says that better understanding of these basic mechanisms could have broad implications for studying health and disease because gene regulation is such a fundamental biological process.

“When we learn more about basic genetic processes, we can apply this fundamental knowledge to so many disorders and open up unexplored avenues for therapies.”